The flavivirus West Nile (WN) virus historically circulated only in the Middle East, Far East, Africa, and southern Europe. The primary life cycle requires birds or horses and local arthropod vectors. In humans, WN virus typically causes a severe fever-arthralgia-rash syndrome but also has a propensity to invade the CNS and cause meningoencephalitis or encephalitis, especially in the elderly (Beasley, D. L. et al. 2002 Virology 296:17-23; Sampathkumar P. 2003 Mayo Clin Proc 78:1137-1143). In the summer of 1999, WN virus infections of birds and humans were detected in New York City, indicating the presence of this pathogen on the American continent for the first time (Centers for Disease Control and Prevention 1999 MMWR Morb Mortal Wkly Rep 48:845-849; Lanciotti, R. S. et al. 1999 Science 286:2333-2337). Since 1999, disease has recurred annually in the United States, reaching epidemic proportions in focal areas of the Eastern and mid-western states during 2002 (Centers for Disease Control and Prevention 2002 MMWR Morb Mortal Wkly Rep 51:1129-1133). WN virus continues to pose a serious threat to the public health, since the vector species are present throughout the North American continent, and since there is no vaccine available.
Flavivirus positive-strand genome RNA is about 10.5 kb in total length and contains a single long open reading frame (ORF), encoding three major viral structural proteins and at least seven non-structural (NS) proteins. The ORF is flanked by a 5′ noncoding region (NCR) which is about 100 nucleotides (nt) in length and by a 3′-NCR which is 400 to 800 nucleotides in length (Lindenbach, B. D. and Rice C. M 2001 in Fields Virology, 4th ed., Knipe, D. M. and Howley, P. M. (eds.), Lippincott Williams and Wilkins, New York, pp 991-1041). The 3′-terminal ˜100 nucleotides of the 3′-NCR form two adjacent small and large stem and loop structures, here referred to collectively as the 3′SL (Brinton, M. A. et al. 1986 Virology 153:113-121; Grange, T. M. et al. 1985 FEBS Lett 188:159-163; Irie, K. et al. 1989 Gene 75:197-211; Men, R. et al. 1996 J Virol 70:3930-3937; Mohan, P. M. and Padmanabhan, R. 1991 Gene 108:185-191; Rice, C. M. et al. 1985 Science 229:726-735; Wengler, G. and Castle, E. 1986 J Gen Virol 67:1183-1188). This secondary structure is conserved among all flavivirus genomes. The 3′SL is essential for virus replication (Men, R. et al. 1996 J Virol 70:3930-3937; Zeng, L. et al. 1998 J Virol 72:7510-7522) and has specific affinity for host cellular proteins (Blackwell, J. L. and Brinton, M. A. 1996 J Virol 69:5650-5658; Blackwell, J. L. and Brinton, M. A. 1997 J Virol 71:6433-6444; De Nova-Campo, M. et al. 2002 Virology 295:337-347; Ito, T. and Lai, M. M. 1997 J Virol 71:8698-8706; Ta, M. and Vrati, S. 2000 J Virol 74:5108-5115) and for viral NS proteins of the replication complex (Chen, C.-J. et al. 1997 J Virol 71:3466-3473), including NS5 (Tan, B. H. et al. 1996 Virology 216:317-325), the viral RNA-dependent RNA polymerase.